Should I leave the existing ventilation fans in when getting a new metal roof installed?
You have to have ventilation. Metal is not an insulator, it’s a conductor. If it’s shiny it will reflect, but it won’t stay shiny. If there is insulation under the metal, then the reflective quality will be helpful, but if not, the metal will heat up and it will get hotter than hell in your attic, and make your AC work harder. The more ventilation you have, the better. Ridge vents are good. The problem with your existing fans is that they were made to install on a shingle roof, and the flange is probably full of nail holes and roofing cement, and hard to tie in on a metal roof. They can probably be modified in various ways, (e.g. curb mounted), by a good sheetmetal mechanic to work with a metal roof, and hopefully, your roofer is a good sheetmetal mechanic. Alternatively you could put gable fans, if you have gables.
